From 472b4f1fe768d352d2674abfcef23ff8c1f375f1 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Tue, 25 Apr 2023 17:44:09 +0100
Subject: [PATCH] When linting, add quay.io when we think it is a biocontainer

---
 nf_core/modules/lint/main_nf.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 493fa9eed..6aea64705 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -307,6 +307,9 @@ def check_process_section(self, lines, fix_version, progress_bar):
             else:
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
                 docker_tag = None
+            if l.startswith("biocontainers/"):
+                # When we think it is a biocontainer, assume we are querying quay.io/biocontainers and insert quay.io as prefix
+                l = "quay.io/" + l
             url = urlparse(l.split("'")[0])
             # lint double quotes
             if l.count('"') > 2: